private static BreakEndAdjacency Flip(this BreakEndAdjacency adjacency)
{
var origin = new BreakPoint(adjacency.Partner.Chromosome, adjacency.Partner.Position, !adjacency.Partner.OnReverseStrand);
var partner = new BreakPoint(adjacency.Origin.Chromosome, adjacency.Origin.Position, !adjacency.Origin.OnReverseStrand);
return(new BreakEndAdjacency(origin, partner));
}
private static BreakEndAdjacency[] CreateFromDuplication(IChromosomeInterval interval)
{
// 1 1 . N ]1:10]N
var origin = new BreakPoint(interval.Chromosome, interval.End, false);
var remote = new BreakPoint(interval.Chromosome, interval.Start - 1, false);
var adjacency = new BreakEndAdjacency(origin, remote);
return(new[] { adjacency, adjacency.Flip() });
}
private static BreakEndAdjacency[] CreateFromInversion(IChromosomeInterval interval)
{
// 1 10 . N N]1:20]
// 1 11 . N [1:21[N
var origin = new BreakPoint(interval.Chromosome, interval.Start - 1, false);
var remote = new BreakPoint(interval.Chromosome, interval.End, true);
var adjacency = new BreakEndAdjacency(origin, remote);
var origin2 = new BreakPoint(interval.Chromosome, interval.End + 1, true);
var remote2 = new BreakPoint(interval.Chromosome, interval.Start, false);
var adjacency2 = new BreakEndAdjacency(origin2, remote2);
return(new[] { adjacency, adjacency2 });
}
private static BreakEndAdjacency[] ConvertTranslocation(ISimpleVariant variant, Regex regex,
bool onReverseStrand, int partnerBracketIndex, IDictionary <string, IChromosome> refNameToChromosome)
{
var match = regex.Match(variant.AltAllele);
if (!match.Success)
{
throw new InvalidDataException($"Unable to successfully parse the complex rearrangements for the following allele: {variant.AltAllele}");
}
bool partnerOnReverseStrand = match.Groups[partnerBracketIndex].Value == ReverseBracket;
var partnerPosition = Convert.ToInt32(match.Groups[3].Value);
string partnerReferenceName = match.Groups[2].Value;
var partnerChromosome = ReferenceNameUtilities.GetChromosome(refNameToChromosome, partnerReferenceName);
var origin = new BreakPoint(variant.Chromosome, variant.Start, onReverseStrand);
var partner = new BreakPoint(partnerChromosome, partnerPosition, partnerOnReverseStrand);
return(new[] { new BreakEndAdjacency(origin, partner) });
}
public BreakEndAdjacency(BreakPoint origin, BreakPoint partner)
{
Origin = origin;
Partner = partner;
}